Related papers: Gene expression from polynomial dynamics in the 2-…
Stem cell regeneration is a vital biological process in self-renewing tissues, governing development and tissue homeostasis. Gene regulatory network dynamics are pivotal in controlling stem cell regeneration and cell type transitions.…
We treat the problem of characterizing in a systematic way the qualitative features of two-dimensional dynamical systems. To that end, we construct a representation of the topological features of phase portraits by means of diagrams that…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Multidimensional genetic programming represents candidate solutions as sets of programs, and thereby provides an interesting framework for exploiting building block identification. Towards this goal, we investigate the use of machine…
Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable…
In order to understand the complexities of cellular biology, researchers are interested in two important metrics: the genetic expression information of cells and their spatial coordinates within a tissue sample. However, state-of-the art…
Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…
Solving Quadratic equation is one of the intrinsic interests as it is the simplest nonlinear equations. A novel approach for solving Quadratic Equation based on Genetic Algorithms (GAs) is presented. Genetic Algorithms (GAs) are a technique…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
In this brief article I show how the notion of coarse graining and the Renormalization Group enter naturally in the dynamics of genetic systems, in particular in the presence of recombination. I show how the latter induces a dynamics…
A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with…
This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
A genetic algorithm is suitable for exploring large search spaces as it finds an approximate solution. Because of this advantage, genetic algorithm is effective in exploring vast and unknown space such as molecular search space. Though the…
Neural networks and evolutionary computation have a rich intertwined history. They most commonly appear together when an evolutionary algorithm optimises the parameters and topology of a neural network for reinforcement learning problems,…
In cellular reprogramming, almost all epigenetic memories of differentiated cells are erased by the overexpression of few genes, regaining pluripotency, potentiality for differentiation. Considering the interplay between oscillatory gene…